Variant report

Variant	rs9366917
Chromosome Location	chr6:36790666-36790667
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36789119..36791202-chr6:36794316..36796954,2	MCF-7	breast:
2	chr6:36779359..36780999-chr6:36789470..36790990,2	K562	blood:
3	chr6:36185667..36187544-chr6:36788292..36790992,2	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12528273	0.81[JPT][hapmap]
rs2293393	0.83[JPT][hapmap]
rs236358	0.82[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs236373	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs236385	0.89[JPT][hapmap]
rs236386	0.89[JPT][hapmap]
rs460539	0.90[JPT][hapmap];0.84[MEX][hapmap]
rs6910832	0.84[JPT][hapmap]
rs9394384	0.81[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1033261	chr6:36687424-36837315	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv5261	chr6:36754545-36798824	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Active TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	esv3396486	chr6:36788274-36793172	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9366917	MTCH1	cis	brain	seeQTL
rs9366917	PXT1	cis	brain	seeQTL
rs9366917	PNPLA1	cis	parietal	SCAN
rs9366917	LRFN2	cis	cerebellum	SCAN
rs9366917	CCDC50	trans	brain	seeQTL
rs9366917	FGD2	cis	brain	seeQTL
rs9366917	SMN2	trans	brain	seeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36777000-36797800	Weak transcription	Pancreas	Pancrea
2	chr6:36779000-36794000	Weak transcription	Brain Germinal Matrix	brain
3	chr6:36779400-36797600	Weak transcription	Fetal Brain Female	brain
4	chr6:36781600-36794200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr6:36786000-36790800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:36787000-36791200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:36787400-36796400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:36788000-36791000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:36788400-36802400	Weak transcription	Fetal Kidney	kidney
10	chr6:36788600-36792800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:36788800-36791000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:36788800-36792000	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr6:36788800-36793200	Enhancers	Adipose Nuclei	Adipose
14	chr6:36788800-36797200	Enhancers	Right Atrium	heart
15	chr6:36789000-36791800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:36789200-36792400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
17	chr6:36789200-36796400	Enhancers	Left Ventricle	heart
18	chr6:36789400-36790800	Genic enhancers	Right Ventricle	heart
19	chr6:36789400-36792200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:36789400-36793200	Weak transcription	Fetal Intestine Small	intestine
21	chr6:36789400-36794200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:36789400-36794400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:36789400-36796000	Enhancers	K562	blood
24	chr6:36789600-36790800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr6:36789600-36791400	Weak transcription	Spleen	Spleen
26	chr6:36789600-36794000	Enhancers	HUVEC	blood vessel
27	chr6:36789600-36794600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr6:36789800-36794000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:36789800-36794200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:36789800-36794200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:36789800-36794600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:36789800-36802200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr6:36790000-36790800	Genic enhancers	Fetal Muscle Trunk	muscle
34	chr6:36790000-36794200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr6:36790000-36794400	Weak transcription	HMEC	breast
36	chr6:36790000-36794600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:36790200-36794400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr6:36790400-36791000	Enhancers	NH-A	brain
39	chr6:36790400-36791200	Enhancers	Lung	lung
40	chr6:36790400-36793800	Weak transcription	Brain Anterior Caudate	brain
41	chr6:36790400-36794600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
42	chr6:36790600-36790800	Enhancers	Fetal Heart	heart
43	chr6:36790600-36790800	Flanking Bivalent TSS/Enh	HepG2	liver
44	chr6:36790600-36791000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:36790600-36791000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr6:36790600-36791000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:36790600-36791200	Enhancers	Fetal Stomach	stomach
48	chr6:36790600-36791200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
49	chr6:36790600-36791400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr6:36790600-36794200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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